Primary lymphoma of the male genital tract (PLMGT) is rare, and data on its epidemiology and prognosis are lacking. Our study aimed to estimate the incidence and develop a predictive nomogram for PLMGT. We pooled the incidence and survival data of PLMGT over the last 20 years from the Surveillance, Epidemiology, and End Results (SEER) database. Incidence rates were calculated by year of diagnosis, age, race, and histology. Independent prognostic factors selected by Cox regression analysis were used to develop a nomogram for predicting overall survival (OS). Our study enrolled 1312 patients with PLMGT. The overall incidence rate of PLMGT was 0.437/1,000,000 during 2000-2019. OS was associated with age, marital status, histological subtype, Ann Arbor stage, and therapeutic strategy, which were used to construct nomograms to predict 1-, 3-, and 5-year OS rates. Receiver operating characteristic curves, calibration plots, and decision curve analysis showed good performance of the nomogram. Based on the total score of each patient from the nomogram, the patients were clustered into three risk groups, and the risk stratification model was more successful in predicting clinical outcomes than the traditional Ann Arbor staging system. The incidence rate of PLMGT has remained relatively stable over the past two decades. For the OS of patients with PLMGT, we established a novel predictive nomogram involving all independent risk factors obtained from the SEER database and developed a corresponding risk classification system that showed better predictive performance than the Ann Arbor staging system.